[Coldsaturn]

I still have to properly dissect your last playthrough because I was busy compiling Xav's timeline, but I just want to say that the questions you're asking are much more on point than some of your past theories.
A lot of this is a lack of Myth context + Anecdotes and World Underneath (which we would have already been consuming by the time Caleb dropped with Homecoming Wings). You're playing the main story line but remember that Anecdotes, Myths and WU texts work with it in equal measure. You're asking the right questions and making the right assumptions, you're simply missing info. But don't worry about not getting all the answers within the end of Homecoming Wings, because you're not supposed to get them all there.

"What are we?" has been a huge question in some players' circles, and it's interesting that hints and clues were also left in the lyrics of the main OSTs, especially the ones in Chinese. There's a youtuber who does incredibly good analysis taking into consideration the Chinese background of the game, I'll link her videos to you once you've gone through your reading homework.